Multiple sequence alignment - TraesCS3B01G084900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G084900 chr3B 100.000 2597 0 0 1 2597 53522874 53525470 0 4796
1 TraesCS3B01G084900 chr3B 94.453 2037 101 7 570 2597 687040066 687042099 0 3125
2 TraesCS3B01G084900 chr3B 94.362 2022 104 6 566 2584 804661029 804663043 0 3094
3 TraesCS3B01G084900 chr3B 96.837 569 18 0 1 569 180851352 180850784 0 952
4 TraesCS3B01G084900 chr2D 95.882 2040 73 7 566 2597 64508694 64510730 0 3291
5 TraesCS3B01G084900 chrUn 94.927 2050 90 8 560 2597 60558700 60560747 0 3197
6 TraesCS3B01G084900 chr5B 94.894 2037 88 9 570 2597 26059378 26057349 0 3171
7 TraesCS3B01G084900 chr5B 96.837 569 17 1 1 569 150738862 150738295 0 950
8 TraesCS3B01G084900 chr5B 96.485 569 20 0 1 569 153407388 153407956 0 941
9 TraesCS3B01G084900 chr5B 96.485 569 20 0 1 569 176729354 176729922 0 941
10 TraesCS3B01G084900 chr1B 94.690 2034 101 6 570 2597 542264940 542266972 0 3151
11 TraesCS3B01G084900 chr1B 97.012 569 17 0 1 569 162333674 162334242 0 957
12 TraesCS3B01G084900 chr2B 94.654 2039 90 12 565 2597 546410282 546412307 0 3144
13 TraesCS3B01G084900 chr2B 96.661 569 19 0 1 569 448166090 448166658 0 946
14 TraesCS3B01G084900 chr4B 93.762 2036 104 11 570 2597 645967796 645965776 0 3035
15 TraesCS3B01G084900 chr7B 93.731 2026 103 11 569 2584 503449500 503451511 0 3016
16 TraesCS3B01G084900 chr6B 96.661 569 19 0 1 569 502427992 502427424 0 946
17 TraesCS3B01G084900 chr6B 96.485 569 20 0 1 569 233147059 233146491 0 941
18 TraesCS3B01G084900 chr6B 96.485 569 20 0 1 569 259054879 259054311 0 941


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G084900 chr3B 53522874 53525470 2596 False 4796 4796 100.000 1 2597 1 chr3B.!!$F1 2596
1 TraesCS3B01G084900 chr3B 687040066 687042099 2033 False 3125 3125 94.453 570 2597 1 chr3B.!!$F2 2027
2 TraesCS3B01G084900 chr3B 804661029 804663043 2014 False 3094 3094 94.362 566 2584 1 chr3B.!!$F3 2018
3 TraesCS3B01G084900 chr3B 180850784 180851352 568 True 952 952 96.837 1 569 1 chr3B.!!$R1 568
4 TraesCS3B01G084900 chr2D 64508694 64510730 2036 False 3291 3291 95.882 566 2597 1 chr2D.!!$F1 2031
5 TraesCS3B01G084900 chrUn 60558700 60560747 2047 False 3197 3197 94.927 560 2597 1 chrUn.!!$F1 2037
6 TraesCS3B01G084900 chr5B 26057349 26059378 2029 True 3171 3171 94.894 570 2597 1 chr5B.!!$R1 2027
7 TraesCS3B01G084900 chr5B 150738295 150738862 567 True 950 950 96.837 1 569 1 chr5B.!!$R2 568
8 TraesCS3B01G084900 chr5B 153407388 153407956 568 False 941 941 96.485 1 569 1 chr5B.!!$F1 568
9 TraesCS3B01G084900 chr5B 176729354 176729922 568 False 941 941 96.485 1 569 1 chr5B.!!$F2 568
10 TraesCS3B01G084900 chr1B 542264940 542266972 2032 False 3151 3151 94.690 570 2597 1 chr1B.!!$F2 2027
11 TraesCS3B01G084900 chr1B 162333674 162334242 568 False 957 957 97.012 1 569 1 chr1B.!!$F1 568
12 TraesCS3B01G084900 chr2B 546410282 546412307 2025 False 3144 3144 94.654 565 2597 1 chr2B.!!$F2 2032
13 TraesCS3B01G084900 chr2B 448166090 448166658 568 False 946 946 96.661 1 569 1 chr2B.!!$F1 568
14 TraesCS3B01G084900 chr4B 645965776 645967796 2020 True 3035 3035 93.762 570 2597 1 chr4B.!!$R1 2027
15 TraesCS3B01G084900 chr7B 503449500 503451511 2011 False 3016 3016 93.731 569 2584 1 chr7B.!!$F1 2015
16 TraesCS3B01G084900 chr6B 502427424 502427992 568 True 946 946 96.661 1 569 1 chr6B.!!$R3 568
17 TraesCS3B01G084900 chr6B 233146491 233147059 568 True 941 941 96.485 1 569 1 chr6B.!!$R1 568
18 TraesCS3B01G084900 chr6B 259054311 259054879 568 True 941 941 96.485 1 569 1 chr6B.!!$R2 568

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
776 777 0.102663 TTCAGACCGTTGCACGTGTA 59.897 50.0 18.38 10.46 40.58 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2042 0.036765 CCTAGTGGTTACCAGCGCAA 60.037 55.0 11.47 0.0 32.34 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 7.734924 TGCTAGACCATGAAAATGATATGTC 57.265 36.000 0.00 0.00 0.00 3.06
163 164 8.115384 TCCATGAATGAAAGAAGGGAAATAGAA 58.885 33.333 0.00 0.00 0.00 2.10
261 262 2.280524 TGACCCCGTGTTTGAGCG 60.281 61.111 0.00 0.00 0.00 5.03
418 419 8.143193 GCTATTGGATATACTCTGGATGATCTG 58.857 40.741 0.00 0.00 0.00 2.90
436 437 1.450312 GAAGGGCATCAGTCCCACG 60.450 63.158 0.48 0.00 46.36 4.94
611 612 1.283347 AGTGGTGTCCATCTGCTCAT 58.717 50.000 0.00 0.00 35.28 2.90
699 700 1.372087 CTTTGGCATCTCCGTCAGGC 61.372 60.000 0.00 0.00 37.80 4.85
773 774 2.157834 TTATTCAGACCGTTGCACGT 57.842 45.000 7.68 0.00 40.58 4.49
776 777 0.102663 TTCAGACCGTTGCACGTGTA 59.897 50.000 18.38 10.46 40.58 2.90
988 992 0.179084 GGCATTGAGATCCCGTTCGA 60.179 55.000 0.00 0.00 0.00 3.71
1046 1050 2.769621 ATGGATGCAGAGCCGGGA 60.770 61.111 2.18 0.00 0.00 5.14
1068 1074 1.609061 CGTGTGGAGATGCCTGTCTTT 60.609 52.381 0.00 0.00 37.63 2.52
1086 1092 3.986006 GTCTGTCCGTGGTGCCGA 61.986 66.667 0.00 0.00 0.00 5.54
1144 1151 4.304110 GAACCACAATCGTCTGTTCTACA 58.696 43.478 0.00 0.00 33.83 2.74
1407 1414 0.179113 GCACTGACAGAGAGCTAGCC 60.179 60.000 12.13 2.81 35.53 3.93
1547 1554 6.767456 TGTTGAAAATGTATGGAAAGGCATT 58.233 32.000 0.00 0.00 33.55 3.56
1609 1616 8.088365 AGAAATTCACCTAGTTTAAATGTTGGC 58.912 33.333 0.00 0.00 0.00 4.52
1707 1724 8.137437 TGAGGAATTCAGAAACTTTTGATCAAC 58.863 33.333 7.89 0.00 0.00 3.18
1716 1733 6.756074 AGAAACTTTTGATCAACGAAATGCAA 59.244 30.769 7.89 0.00 32.26 4.08
1870 1887 2.311463 GTGCCTCAGCTCTGGTAGATA 58.689 52.381 3.75 0.00 40.80 1.98
2025 2042 1.288335 TGGGTTTGTGGTGTTTAGGGT 59.712 47.619 0.00 0.00 0.00 4.34
2056 2073 2.200081 ACCACTAGGACAGATGGCAAT 58.800 47.619 0.00 0.00 38.69 3.56
2099 2116 9.298250 GGAAGGAATGTATACATAGTGAGACTA 57.702 37.037 18.56 0.00 35.10 2.59
2144 2164 3.635836 TGAGACCATGAATGTTTGCACAA 59.364 39.130 0.00 0.00 36.16 3.33
2185 2205 6.652481 TCCTTTGTTTTGCACTGAAATTTTGA 59.348 30.769 0.00 0.00 0.00 2.69
2385 2412 6.770303 TCATTAATGACAACCACAAGTTCTCA 59.230 34.615 14.23 0.00 37.71 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 7.886629 TCTATTTCCCTTCTTTCATTCATGG 57.113 36.000 0.00 0.00 0.00 3.66
173 174 6.206634 TGTTGCAGAATAGGTTCCTGTTTAAG 59.793 38.462 1.12 0.00 34.81 1.85
247 248 0.236449 GTTTACGCTCAAACACGGGG 59.764 55.000 0.00 0.00 38.13 5.73
261 262 5.813080 AAGATTATCAGGCAACGGTTTAC 57.187 39.130 0.00 0.00 46.39 2.01
418 419 1.450312 CGTGGGACTGATGCCCTTC 60.450 63.158 0.00 0.00 46.19 3.46
641 642 1.077716 GCACGGACTAGGGGCAAAT 60.078 57.895 0.00 0.00 0.00 2.32
699 700 0.243636 GGGCCGAGTCAAAATGTTGG 59.756 55.000 0.00 0.00 35.29 3.77
739 740 3.882888 CTGAATAAAATTGGGCGCCTCTA 59.117 43.478 28.56 13.87 0.00 2.43
747 748 4.173256 GCAACGGTCTGAATAAAATTGGG 58.827 43.478 0.00 0.00 0.00 4.12
773 774 2.925706 TGGGTCCCGCAAGCTACA 60.926 61.111 2.65 0.00 0.00 2.74
848 851 2.742372 GTTGCCGTGATCACCGCT 60.742 61.111 30.34 0.00 36.68 5.52
856 859 2.243957 CGTGCTCTTGTTGCCGTGA 61.244 57.895 0.00 0.00 0.00 4.35
938 942 1.913762 ACAGCTAGCTTCCCACCGT 60.914 57.895 16.46 5.02 0.00 4.83
972 976 1.409427 GGAGTCGAACGGGATCTCAAT 59.591 52.381 0.00 0.00 0.00 2.57
988 992 0.820871 GAAGACATGGAGCTCGGAGT 59.179 55.000 7.83 5.42 0.00 3.85
1030 1034 3.473647 CTCCCGGCTCTGCATCCA 61.474 66.667 0.00 0.00 0.00 3.41
1046 1050 2.267006 CAGGCATCTCCACACGCT 59.733 61.111 0.00 0.00 37.29 5.07
1068 1074 4.293648 CGGCACCACGGACAGACA 62.294 66.667 0.00 0.00 0.00 3.41
1086 1092 1.513158 CCTCCGATCAACACTCGCT 59.487 57.895 0.00 0.00 34.84 4.93
1144 1151 1.452651 CCCCATTCTCGCTGCACAT 60.453 57.895 0.00 0.00 0.00 3.21
1407 1414 4.245660 TCTTCAACATCCTAAGCTCAACG 58.754 43.478 0.00 0.00 0.00 4.10
1707 1724 8.854979 TGGAATAATTCATTAGTTGCATTTCG 57.145 30.769 0.00 0.00 0.00 3.46
1716 1733 7.615365 TGTTTGGCTCTGGAATAATTCATTAGT 59.385 33.333 0.00 0.00 0.00 2.24
1838 1855 2.159282 GCTGAGGCACATTTTCCATGAG 60.159 50.000 0.00 0.00 38.54 2.90
1870 1887 9.030452 TCATTTATTTTGGCACTAGGTGTAAAT 57.970 29.630 0.00 0.00 35.75 1.40
2025 2042 0.036765 CCTAGTGGTTACCAGCGCAA 60.037 55.000 11.47 0.00 32.34 4.85
2056 2073 3.521937 CCTTCCCTACCCATGTCAAACTA 59.478 47.826 0.00 0.00 0.00 2.24
2144 2164 0.759346 AGGAAAACCACTCTCACGCT 59.241 50.000 0.00 0.00 0.00 5.07
2185 2205 2.429250 CGTTTTCAACCTTCCAACCCTT 59.571 45.455 0.00 0.00 0.00 3.95
2385 2412 4.082125 CCCTAAACCAAGTCATGAAGCTT 58.918 43.478 0.00 0.00 0.00 3.74


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.